diff medaka_consensus.xml @ 10:1ca4ce7241fd draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"

--- a/medaka_consensus.xml	Mon Mar 29 20:06:44 2021 +0000
+++ b/medaka_consensus.xml	Thu Apr 22 20:25:13 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="medaka_consensus_pipeline" name="medaka consensus pipeline" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
+<tool id="medaka_consensus_pipeline" name="medaka consensus pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>Assembly polishing via neural networks</description>
     <macros>
         <import>macros.xml</import>
@@ -11,9 +11,6 @@
 -m ${m}
 -b $b
 -o results
-#if 'draft' in str($out).split(',') or 'variants' in str($out).split(',') or 'polished' in str($out).split(',')
-    -v
-#end if
 -t \${GALAXY_SLOTS:-4}
 ## required
 -i '$i'
@@ -26,14 +23,13 @@
         <param argument="-d" type="data" format="fasta,fasta.gz" label="Select assembly" help="The input assembly should be preprocessed with racon."/>
         <expand macro="model"/>
         <expand macro="b"/>
+        <param argument="-g" type="boolean" truevalue="-g" falsevalue="" label="Don't fill gaps in consensus with draft sequence?" checked="false" />
         <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="'Draft To Consensus', 'Variants' and 'Polished regions in draft coordinates' are generated using the parameter -v.">
             <option value="consensus" selected="true">Consensus</option>
             <option value="probs" selected="true">Consensus probabilities</option>
             <option value="calls" selected="true">Calls to draft</option>
-            <option value="draft">Draft to consensus</option>
-            <option value="variants">Variants</option>
-            <option value="polished">Polished regions in draft coordinates</option>
             <option value="log">Log</option>
+            <option value="gaps">Gap regions in draft</option>
         </param>
     </inputs>
     <outputs>
@@ -47,15 +43,8 @@
         <data name="out_calls" format="bam" from_work_dir="results/calls_to_draft.bam" label="${tool.name} on ${on_string}: Calls to draft">
             <filter>'calls' in out</filter>
         </data>
-        <!-- optional with parameter -v -->
-        <data name="out_draft" format="txt" from_work_dir="results/draft_to_consensus.chain" label="${tool.name} on ${on_string}: Draft to consensus">
-            <filter>'draft' in out</filter>
-        </data>
-        <data name="out_variants" format="vcf_bgzip" from_work_dir="results/variants.vcf.gz" label="${tool.name} on ${on_string}: Variants">
-            <filter>'variants' in out</filter>
-        </data>
-        <data name="out_polished" format="bed" from_work_dir="results/polished_regions_in_draft_coords.bed" label="${tool.name} on ${on_string}: Polished regions in Draft">
-            <filter>'polished' in out</filter>
+        <data name="out_gaps" format="bed" from_work_dir="results/consensus.fasta.gaps_in_draft_coords.bed" label="${tool.name} on ${on_string}: Gaps in draft">
+            <filter>'gaps' in out</filter>
         </data>
         <!-- optional -->
         <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
@@ -70,13 +59,13 @@
             <output name="out_consensus">
                 <assert_contents>
                     <has_n_lines n="2"/>
-                    <has_line line=">4_segment0 4:1.0-3792.0"/>
+                    <has_line line=">4"/>
                     <has_text_matching expression=".+GTCAGAATCGCGTTCAGCGCGTTTCAGCGGTGCGTACAATT.+"/>
                 </assert_contents>
             </output>
             <output name="out_probs">
                 <assert_contents>
-                    <has_size value="165271" delta="100"/>
+                    <has_size value="165503" delta="100"/>
                 </assert_contents>
             </output>
             <output name="out_calls">
@@ -86,17 +75,16 @@
             </output>
         </test>
         <!-- #2 -->
-        <test expect_num_outputs="7">
+        <test expect_num_outputs="5">
             <param name="i" value="basecalls.fastq"/>
             <param name="d" value="assembly.fasta"/>
             <param name="m" value="r941_min_fast_g303"/>
             <param name="b" value="99"/>
-            <param name="out" value="consensus,probs,calls,draft,variants,polished,log"/>
+            <param name="out" value="consensus,probs,calls,log,gaps"/>
             <output name="out_consensus">
                 <assert_contents>
-                    <has_n_lines n="65"/>
-                    <has_line line=">4 length=3792 depth=114.52x circular=true"/>
-                    <has_line line="ATCTCTTT"/>
+                    <has_n_lines n="2"/>
+                    <has_line line=">4"/> <!-- Replace test -->
                 </assert_contents>
             </output>
             <output name="out_probs">
@@ -109,27 +97,16 @@
                     <has_size value="343197" delta="100"/>
                 </assert_contents>
             </output>
-            <output name="out_draft">
-                <assert_contents>
-                    <has_line line="chain 3788 4 3792 + 0 3792 4 3788 + 0 3788 1"/>
-                    <has_line line="1409 1 0"/>
-                    <has_line line="440 1 0"/>
-                    <has_line line="736 1 0"/>
-                    <has_line line="853 1 0"/>
-                    <has_line line="350"/>
-                </assert_contents>
-            </output>
-            <output name="out_polished">
-                <assert_contents>
-                    <has_size value="9"/>
-                </assert_contents>
-            </output>
-            <output name="out_variants" file="variants.vcf.gz" decompress="true"/>
             <output name="out_log">
                 <assert_contents>
                     <has_line line="Polished assembly written to results/consensus.fasta, have a nice day."/>
                 </assert_contents>
             </output>
+            <output name="out_gaps">
+                <assert_contents>
+                    <has_size value="0" delta="0"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[